Calcium in PDB 4phm: The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids

The structure of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids, PDB code: 4phm was solved by P.J.Rizkallah, R.K.Allemann, S.E.Adams, D.J.Miller, M.B.Hallett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.93 / 2.03
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.410, 79.340, 57.260, 90.00, 91.23, 90.00
R / Rfree (%)	19.7 / 25.1

The structure of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids also contains other interesting chemical elements:

Bromine

(Br)

3 atoms

The binding sites of Calcium atom in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids (pdb code 4phm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids, PDB code: 4phm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:44.0 occ:1.00 O A:HOH432 2.2 39.5 1.0 O A:GLU114 2.3 46.7 1.0 O A:ALA109 2.3 50.6 1.0 O A:HOH457 2.3 49.9 1.0 OD1 A:ASP112 2.4 47.9 1.0 OE2 A:GLU119 2.4 44.7 1.0 OE1 A:GLU119 2.5 46.0 1.0 CD A:GLU119 2.8 44.9 1.0 C A:ALA109 3.4 49.9 1.0 CG A:ASP112 3.4 48.6 1.0 C A:GLU114 3.5 45.6 1.0 OD2 A:ASP112 3.8 45.7 1.0 CA A:ALA109 3.9 47.9 1.0 N A:GLU114 4.2 47.3 1.0 CG A:GLU119 4.3 44.6 1.0 N A:VAL115 4.4 44.0 1.0 CA A:GLU114 4.4 47.0 1.0 N A:GLY110 4.5 52.0 1.0 N A:SER116 4.5 41.8 1.0 CA A:VAL115 4.5 44.2 1.0 CB A:ALA109 4.7 49.0 1.0 N A:ASP112 4.7 49.8 1.0 CB A:ASP112 4.7 49.1 1.0 O A:LEU108 4.7 54.4 1.0 N A:MET113 4.8 50.4 1.0 C A:GLY110 4.8 55.6 1.0 CA A:GLY110 4.8 54.0 1.0 O A:HOH406 4.9 59.8 1.0 N A:ASP111 4.9 56.9 1.0 C A:VAL115 4.9 41.3 1.0 CA A:ASP112 5.0 49.6 1.0 OG A:SER116 5.0 43.7 1.0 C A:ASP112 5.0 49.0 1.0

Calcium binding site 2 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:45.2 occ:1.00 O A:LYS158 2.1 40.8 1.0 OD1 A:ASP152 2.3 40.0 1.0 O A:HOH412 2.3 40.0 1.0 OD1 A:ASP154 2.4 52.8 1.0 OG1 A:THR156 2.4 42.0 1.0 OE1 A:GLU163 2.5 43.8 1.0 OE2 A:GLU163 3.0 47.2 1.0 CD A:GLU163 3.1 45.6 1.0 CG A:ASP154 3.3 55.2 1.0 C A:LYS158 3.4 39.1 1.0 CG A:ASP152 3.4 41.9 1.0 OD2 A:ASP154 3.5 58.4 1.0 CB A:THR156 3.6 45.6 1.0 CG2 A:THR156 3.9 49.8 1.0 N A:THR156 3.9 50.2 1.0 N A:GLY160 4.0 41.7 1.0 N A:LYS158 4.1 40.9 1.0 OE1 A:GLU114 4.1 58.2 1.0 OE2 A:GLU114 4.2 55.4 1.0 CA A:ASP152 4.2 43.6 1.0 CB A:ASP152 4.2 39.4 1.0 CA A:LEU159 4.2 40.8 1.0 N A:LEU159 4.2 38.4 1.0 CA A:THR156 4.3 46.6 1.0 CA A:LYS158 4.3 40.4 1.0 OD2 A:ASP152 4.4 44.3 1.0 CD A:GLU114 4.5 54.6 1.0 N A:THR155 4.5 53.3 1.0 C A:LEU159 4.5 39.9 1.0 CG A:GLU163 4.6 43.1 1.0 C A:ASP152 4.6 45.8 1.0 CB A:ASP154 4.6 55.1 1.0 N A:GLY157 4.7 44.3 1.0 N A:ASP154 4.7 51.2 1.0 C A:THR156 4.8 44.0 1.0 C A:ASP154 4.8 52.9 1.0 CA A:ASP154 5.0 53.3 1.0 CA A:GLY160 5.0 43.0 1.0 O A:ASP152 5.0 47.8 1.0

Calcium binding site 3 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:52.4 occ:1.00 OD1 A:ASP182 2.1 48.2 1.0 O A:HOH436 2.1 54.8 1.0 O A:THR188 2.4 54.4 1.0 OD1 A:ASP184 2.4 63.1 1.0 OG A:SER186 2.4 50.0 1.0 OE1 A:GLU193 2.6 50.3 1.0 OE2 A:GLU193 2.7 53.5 1.0 CD A:GLU193 3.0 51.3 1.0 CG A:ASP184 3.3 64.8 1.0 CG A:ASP182 3.3 49.3 1.0 CB A:SER186 3.5 52.0 1.0 OD2 A:ASP184 3.6 65.9 1.0 C A:THR188 3.6 50.2 1.0 N A:SER186 3.9 55.1 1.0 OG1 A:THR188 4.1 44.0 1.0 CA A:ASP182 4.1 51.4 1.0 OD2 A:ASP182 4.1 48.4 1.0 CB A:ASP182 4.2 49.7 1.0 N A:CYS190 4.2 54.9 1.0 CA A:SER186 4.2 53.6 1.0 CA A:ILE189 4.4 50.2 1.0 N A:THR188 4.4 47.9 1.0 N A:ILE189 4.4 47.9 1.0 C A:ASP182 4.5 57.2 1.0 CG A:GLU193 4.5 51.6 1.0 CA A:THR188 4.6 46.7 1.0 N A:ASP184 4.6 68.2 1.0 CB A:ASP184 4.6 67.6 1.0 C A:ILE189 4.8 49.5 1.0 N A:ARG185 4.8 63.9 1.0 N A:GLY187 4.8 51.9 1.0 C A:SER186 4.8 52.6 1.0 O A:ASP182 4.9 54.5 1.0 N A:THR183 4.9 64.3 1.0 C A:ASP184 4.9 64.8 1.0 CA A:ASP184 4.9 67.8 1.0 CB A:THR188 4.9 46.3 1.0 CB A:CYS190 5.0 56.7 1.0

Calcium binding site 4 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:37.5 occ:1.00 OD1 A:ASP137 2.3 45.2 1.0 O A:HOH451 2.3 38.9 1.0 OD1 A:ASN228 2.4 36.0 1.0 OD1 A:ASP227 2.4 37.1 1.0 OD2 A:ASP227 2.5 38.1 1.0 O A:HOH418 2.5 37.0 1.0 OD2 A:ASP225 2.6 37.3 1.0 OD1 A:ASP225 2.7 33.7 1.0 CG A:ASP227 2.8 34.2 1.0 CG A:ASP225 3.0 37.9 1.0 CG A:ASP137 3.2 48.9 1.0 CG A:ASN228 3.3 33.4 1.0 OD2 A:ASP137 3.4 51.8 1.0 ND2 A:ASN228 3.8 33.2 1.0 N A:ASN228 4.1 32.8 1.0 CB A:ASP227 4.2 34.3 1.0 CB A:ASN228 4.3 31.7 1.0 N A:ASP137 4.4 42.8 1.0 O B:HOH430 4.5 40.2 1.0 CB A:ASP137 4.5 47.4 1.0 CB A:ASP225 4.5 38.4 1.0 CA A:ASN228 4.7 31.6 1.0 OD2 B:ASP142 4.7 65.8 1.0 O A:GLY138 4.7 44.1 1.0 OG1 A:THR136 4.8 43.6 1.0 O A:HOH420 4.8 45.8 1.0 C A:ASP227 4.8 31.2 1.0 CA A:ASP227 4.9 32.9 1.0 N A:ASP227 4.9 33.7 1.0 CA A:ASP137 5.0 46.5 1.0

Calcium binding site 5 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:36.9 occ:1.00 O B:HOH468 2.2 34.3 1.0 O B:GLU114 2.3 30.5 1.0 OD1 B:ASP112 2.4 39.1 1.0 O B:HOH442 2.4 36.3 1.0 OE1 B:GLU119 2.4 30.6 1.0 OE2 B:GLU119 2.5 33.7 1.0 O B:ALA109 2.5 44.5 1.0 CD B:GLU119 2.8 32.9 1.0 CG B:ASP112 3.3 38.0 1.0 C B:ALA109 3.5 39.4 1.0 C B:GLU114 3.5 31.8 1.0 OD2 B:ASP112 3.5 41.8 1.0 CA B:ALA109 3.9 39.0 1.0 N B:GLU114 4.2 40.9 1.0 CG B:GLU119 4.3 31.9 1.0 N B:SER116 4.3 28.4 1.0 N B:VAL115 4.4 30.0 1.0 O B:HOH476 4.4 48.8 1.0 CA B:VAL115 4.5 31.9 1.0 CA B:GLU114 4.5 36.4 1.0 N B:GLY110 4.6 39.4 1.0 O B:HOH478 4.6 61.6 1.0 N B:ASP112 4.6 41.8 1.0 CB B:ALA109 4.6 38.4 1.0 CB B:ASP112 4.7 39.3 1.0 N B:MET113 4.7 43.3 1.0 O B:LEU108 4.7 37.0 1.0 CA B:GLY110 4.8 41.2 1.0 C B:GLY110 4.8 43.4 1.0 C B:VAL115 4.8 30.1 1.0 OG B:SER116 4.9 28.9 1.0 CB B:SER116 5.0 28.7 1.0 N B:ASP111 5.0 47.6 1.0 CD B:LYS158 5.0 37.5 1.0 C B:ASP112 5.0 41.1 1.0

Calcium binding site 6 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:37.2 occ:1.00 OD1 B:ASP154 2.2 46.9 1.0 O B:LYS158 2.3 31.0 1.0 OD1 B:ASP152 2.3 33.5 1.0 O B:HOH439 2.4 34.6 1.0 OG1 B:THR156 2.4 38.4 1.0 OE1 B:GLU163 2.5 40.5 1.0 OE2 B:GLU163 2.7 40.3 1.0 CD B:GLU163 3.0 39.5 1.0 CG B:ASP154 3.2 52.1 1.0 C B:LYS158 3.5 30.6 1.0 CG B:ASP152 3.5 35.3 1.0 OD2 B:ASP154 3.5 55.4 1.0 CB B:THR156 3.6 44.4 1.0 N B:THR156 3.8 42.2 1.0 CG2 B:THR156 4.0 44.8 1.0 OE1 B:GLU114 4.1 54.1 1.0 N B:GLY160 4.1 34.6 1.0 CA B:ASP152 4.2 32.2 1.0 CA B:LEU159 4.2 33.2 1.0 CA B:THR156 4.3 42.6 1.0 N B:LYS158 4.3 33.1 1.0 CB B:ASP152 4.3 32.9 1.0 N B:LEU159 4.3 32.4 1.0 OD2 B:ASP152 4.3 36.2 1.0 OE2 B:GLU114 4.4 50.4 1.0 CG B:GLU163 4.5 38.2 1.0 CA B:LYS158 4.5 30.2 1.0 C B:ASP152 4.6 36.3 1.0 CB B:ASP154 4.6 50.3 1.0 CD B:GLU114 4.6 50.4 1.0 N B:THR155 4.6 51.4 1.0 N B:ASP154 4.6 46.0 1.0 C B:LEU159 4.6 32.7 1.0 N B:GLY157 4.7 41.8 1.0 C B:THR156 4.8 43.0 1.0 C B:ASP154 4.8 52.3 1.0 C B:THR155 4.9 47.1 1.0 CA B:ASP154 4.9 50.0 1.0

Calcium binding site 7 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:41.0 occ:1.00 OG B:SER186 2.2 39.4 1.0 O B:HOH443 2.2 61.5 1.0 O B:THR188 2.3 31.3 1.0 OD1 B:ASP184 2.3 40.6 1.0 OD1 B:ASP182 2.3 36.0 1.0 OE2 B:GLU193 2.4 33.4 1.0 OE1 B:GLU193 2.6 32.9 1.0 CD B:GLU193 2.9 31.9 1.0 CG B:ASP184 3.3 43.4 1.0 CG B:ASP182 3.4 35.8 1.0 CB B:SER186 3.4 42.5 1.0 C B:THR188 3.5 29.5 1.0 OD2 B:ASP184 3.6 43.0 1.0 CA B:ASP182 3.9 35.5 1.0 N B:SER186 4.0 47.2 1.0 CB B:ASP182 4.1 37.0 1.0 C B:ASP182 4.2 40.4 1.0 OG1 B:THR188 4.3 37.7 1.0 OD2 B:ASP182 4.3 35.2 1.0 N B:THR188 4.3 32.1 1.0 CA B:ILE189 4.3 31.6 1.0 CA B:SER186 4.3 45.5 1.0 N B:ILE189 4.3 29.6 1.0 CG B:GLU193 4.4 34.1 1.0 N B:ASP184 4.4 47.0 1.0 CA B:THR188 4.5 32.3 1.0 N B:CYS190 4.5 37.8 1.0 N B:THR183 4.6 42.0 1.0 CB B:ASP184 4.7 47.8 1.0 N B:ARG185 4.8 45.2 1.0 O B:ASP182 4.8 36.4 1.0 SG B:CYS190 4.8 49.3 1.0 O B:HOH408 4.8 47.1 1.0 C B:ILE189 4.9 31.5 1.0 CA B:ASP184 4.9 46.7 1.0 N B:GLY187 5.0 39.1 1.0 C B:ASP184 5.0 46.2 1.0

Calcium binding site 8 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca305 b:30.4 occ:1.00 O B:HOH435 2.1 28.0 1.0 OD2 B:ASP227 2.3 29.9 1.0 OD1 B:ASN228 2.4 31.2 1.0 O A:HOH413 2.4 25.6 1.0 OD2 B:ASP225 2.4 31.9 1.0 OD1 B:ASP227 2.5 29.4 1.0 OD1 B:ASP225 2.5 28.5 1.0 OD1 B:ASP137 2.6 32.5 1.0 CG B:ASP227 2.8 27.2 1.0 CG B:ASP225 2.8 32.7 1.0 CG B:ASP137 3.4 38.3 1.0 CG B:ASN228 3.4 32.2 1.0 OD2 B:ASP137 3.7 42.7 1.0 N B:ASN228 4.1 25.7 1.0 ND2 B:ASN228 4.2 32.9 1.0 CB B:ASP227 4.2 25.6 1.0 O B:HOH447 4.3 38.0 1.0 CB B:ASP225 4.3 29.8 1.0 O B:HOH453 4.3 33.6 1.0 CB B:ASN228 4.4 28.7 1.0 NH1 A:ARG145 4.4 49.1 1.0 N B:ASP137 4.5 30.4 1.0 CA B:ASN228 4.7 26.6 1.0 CG2 B:THR136 4.7 31.3 1.0 CB B:ASP137 4.7 34.4 1.0 O B:GLY138 4.7 28.7 1.0 OD1 A:ASP142 4.7 55.8 1.0 C B:ASP227 4.8 25.1 1.0 CA B:ASP227 4.8 26.1 1.0 O B:HOH461 4.9 38.7 1.0 N B:ASP227 4.9 24.9 1.0 O B:HOH433 4.9 37.2 1.0

S.E.Adams, P.J.Rizkallah, D.J.Miller, E.J.Robinson, M.B.Hallett, R.K.Allemann. The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids. J.Struct.Biol. V. 187 236 2014.
ISSN: ESSN 1095-8657
PubMed: 25086406
DOI: 10.1016/J.JSB.2014.07.004